A multi-material 3D printed microfluidic reactor with integrated heating is presented, which was applied within a manifold for the colorimetric determination of ammonium in natural waters. Graphene doped polymer was used to provide localised heating when connected to a power source, achieving temperatures of up to 120 °C at 12 V, 0.7 A. An electrically insulating layer of acrylonitrile butadiene styrene (ABS) polymer or a new microdiamond-ABS polymer composite was used as a heater coating. The microdiamond polymer composite provided higher thermal conductivity and uniform heating of the serpentine microreactor which resulted in greater temperature control and accuracy in comparison to pure ABS polymer. The developed heater was then applied and demonstrated using a modified Berthelot reaction for ammonium analysis, in which the microreactor was configured at a predetermined optimised temperature. A 5-fold increase in reaction speed was observed compared to previously reported reaction rates. A simple flow injection analysis set up, comprising the microfluidic heater along with an LED-photodiode based optical detector, was assembled for ammonium analysis. Two river water samples and two blind ammonium standards were analysed and estimated concentrations were compared to concentrations determined using benchtop IC. The highest relative error observed following the analysis of the environmental samples was 11% and for the blind standards was 5%.